Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2308 to 2357 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2308	60s ribosomal protein l7. [source:swissprot;acc:p18124]	3976.92	3804.85	1.04522	
2309	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [source:swissprot;acc:o76062]	6960.96	7273.7	1.04493	
2310	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [source:swissprot;acc:q14739]	6960.96	7273.7	1.04493	
2311	solute carrier family 27 member 3; fatty acid transport protein 3. [source:refseq;acc:nm_024330]	6961.19	7273.93	1.04493	
2312	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [source:swissprot;acc:o14975]	6960.26	7273.01	1.04493	
2313	disrupter of silencing 10. [source:refseq;acc:nm_020368]	6960.96	7273.7	1.04493	
2314	very long-chain acyl-coa synthetase homolog 1. [source:refseq;acc:nm_014031]	6960.99	7273.72	1.04493	
2315	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [source:refseq;acc:nm_012254]	6961.11	7273.85	1.04493	
2316	similar to cg7020 gene product (fragment). [source:sptrembl;acc:q96ib4]	6960.74	7273.48	1.04493	
2317	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [source:refseq;acc:nm_005094]	6961.44	7274.17	1.04492	
2318	ubiquitin. [source:swissprot;acc:p02248]	7484.98	7821.11	1.04491	
2319	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	6362.48	6647.42	1.04478	
2320	t54 protein. [source:swissprot;acc:q92917]	6362.48	6647.42	1.04478	
2321	dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [source:swissprot;acc:q9nrf9]	3496.21	3652.28	1.04464	
2322	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [source:swissprot;acc:q15796]	6773.67	7075.51	1.04456	
2323	mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [source:swissprot;acc:q15797]	6773.67	7075.51	1.04456	
2324	cop9 subunit 6 (mov34 homolog, 34 kd). [source:refseq;acc:nm_006833]	6773.67	7075.51	1.04456	
2325	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [source:swissprot;acc:q92940]	6773.67	7075.51	1.04456	
2326	histone deacetylase 11 (hd11). [source:swissprot;acc:q96db2]	6773.67	7075.51	1.04456	
2327	ethanolamine kinase-like protein eki2 (flj10761). [source:swissprot;acc:q9nvf9]	6773.67	7075.51	1.04456	
2328	ethanolamine kinase (ec 2.7.1.82) (eki). [source:swissprot;acc:q9hbu6]	6773.67	7075.51	1.04456	
2329	hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [source:refseq;acc:nm_020232]	6773.67	7075.51	1.04456	
2330	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [source:refseq;acc:nm_006837]	6773.67	7075.51	1.04456	
2331	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [source:swissprot;acc:o15198]	6773.67	7075.51	1.04456	
2332	mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [source:swissprot;acc:q99717]	6773.67	7075.51	1.04456	
2333	thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [source:swissprot;acc:q99757]	6773.67	7075.51	1.04456	
2334	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	5123.89	5350.78	1.04428	
2335	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [source:swissprot;acc:q15005]	5123.89	5350.78	1.04428	
2336	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [source:swissprot;acc:p11172]	5123.89	5350.78	1.04428	
2337	cleft lip and palate associated transmembrane protein 1. [source:refseq;acc:nm_001294]	5123.89	5350.78	1.04428	
2338	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [source:swissprot;acc:p17213]	5123.89	5350.78	1.04428	
2339	phospholipid transfer protein precursor (lipid transfer protein ii). [source:swissprot;acc:p55058]	5123.89	5350.78	1.04428	
2340	alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [source:swissprot;acc:q9ujy1]	5607.81	5855.72	1.04421	
2341	heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [source:swissprot;acc:p04792]	5606.66	5854.45	1.0442	
2342	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [source:swissprot;acc:q9nr19]	7007.72	7317.15	1.04416	
2343	40s ribosomal protein s5. [source:swissprot;acc:p46782]	3672.17	3516.98	1.04413	
2344	carboxypeptidase a5. [source:refseq;acc:nm_080385]	8353.97	8001.45	1.04406	
2345	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	8353.97	8001.45	1.04406	
2346	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	8353.97	8001.45	1.04406	
2347	ral guanine nucleotide exchange factor ralgps1a. [source:refseq;acc:nm_014636]	6480.27	6765.81	1.04406	
2348	ral-a exchange factor ralgps2. [source:refseq;acc:nm_152663]	6480.27	6765.81	1.04406	
2349	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	8353.97	8001.45	1.04406	
2350	stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [source:refseq;acc:nm_005861]	6480.27	6765.81	1.04406	
2351	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	8353.97	8001.45	1.04406	
2352	coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [source:swissprot;acc:o14579]	8493.7	8135.59	1.04402	
2353	signal transducer and activator of transcription 5b. [source:swissprot;acc:p51692]	5516.82	5758.48	1.0438	
2354	signal transducer and activator of transcription 5a. [source:swissprot;acc:p42229]	5516.67	5758.22	1.04379	
2355	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [source:refseq;acc:nm_012301]	5262.6	5492.58	1.0437	
2356	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	5515.12	5755.63	1.04361	
2357	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	5514.85	5755.17	1.04358	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/